PRELIMINARY PROGRAM OF RECOMB'99 April 11-14, Hotel de Lyon Metropole, Lyon, France ------------------------ Saturday, April 10, 1999 ------------------------ 16:00 - 19:00 - Welcome and registration at Lyon Metropole Hotel 18:00 Cocktail offered by the City Hall of Lyon ---------------------- Sunday, April 11, 1999 ---------------------- 8:45 Opening Remarks: Sorin Istrail, General RECOMB Vice-Chair 1999 Program Committee Chair Mireille Regnier, 1999 Conference Chair Ron Shamir, 2000 Program Committee Chair Distinguished New Technologies Lecture - Chair: S. Istrail ---------------------------------------------------------- 9:00 Large DNA Microarrays - the How and the Why Ed Southern 10:00 Short break Session on Gene Expression - Chair: S. Schbath ---------------------------------------------- 10:05 Algorithms for Choosing Differential Gene Expression Experiments R. M. Karp, R. Stoughton, K. Y. Yeung 10:30 An Algorithm for Clustinering cDNAs for Gene Expression Analysis E. Hartuv, A. Schmitt, J. Lange, S. Meirer-Ewert, H. Lehrach, R. Shamir 10:55 A Dictionary Based Approach for Gene Annotation L. Pachter, S. Batzoglou, V. I. Spitkovsky, W. S. Beebee Jr., E. S. Lander, B. Berger, D. J. Kleitman 11:20 Break Session on Sequencing - Chair: R. Karp -------------------------------------- 11:45 De Novo Peptide Sequencing via Tandem Mass Spectrometry: A Graph-Theoretical Approach V. Dancik, T. Addona, K. Clauser, J. Vath, P. A. Pevzner 12:10 On the Power of Universal Bases in Sequencing by Hybridization F. P. Preparata, A. M. Frieze, E. Upfal Lunch: 12:35 - 14:00 -------------------- Distinguished Biology Lecture - Chair: P. Pevzner ------------------------------------------------- 14:00 Whole Genome Association Studies in Humans Daniel Cohen 15:00 Short break Session on Protein Structure - Chair: M. Levitt ----------------------------------------------- 15:05 Recognition of Remote Protein Homologies Using Three-Dimensional Information to Generate a Position Specific Scoring Matrix in the Program 3D-PSSM L. Kelley, R. MacCullum, M. J. E. Sternberg 15:30 A Solvation Potential with Improved Contact Definitions and Optimized by Extensive Threading A. Dombkowski, G. M. Crippen 15:55 Fast Detection of Common Geometric Substructure in Proteins L. P. Chew, D. Huttenlocher, K. Kedem, J. Kleinberg 16:20 Break Plenary Lecture Session - Chair: M. Levitt ------------------------------------------ 16:45 The Past, Present and Future of Protein Structure Prediction John Moult 18:00 - 20:00 Business Meeting ---------------------- Monday, April 12, 1999 ---------------------- Plenary Lecture Session - Chair: R. Karp ---------------------------------------- 8:30 Computational Analysis of Molecular Diversity for Drug Discovery Peter Willett 9:30 Short break Session on Genomic Rearrangements - Chair: R. Shamir ---------------------------------------------------- 9:35 Reconstructing the Pre-Doubling Genome N. El-Mabrouk, D. Bryant, D. Sankoff 10:00 Formulations and Hardness of Multiple Sorting by Reversals A. Caprara 10:25 Probability Models for Genome Rearrangement and Linear Invariants for Phylogenetic Inference D. Sankoff, M. Blanchette 10:50 Break Session on Trees - Chair: A. Guenoche ------------------------------------- 11:15 Modeling Protein Families Using Probabilistic Suffix Trees G. Bejerano, G. Yona 11:40 Faster Reliable Phylogenetic Analysis V. Berry, D. Bryant 12:05 Obtaining Highly Accurate Topology Estimates of Evolutionary Trees from Very Short Sequences D. H. Huson, S. Nettles, T. J. Warnow Lunch: 12:30 - 14:00 -------------------- Plenary Lecture Session - Chair: D. Slonim ------------------------------------------ 14:00 Progress Toward the Whole-Genome Shotgun Sequencing of Drosophilia Gene Myers 15:00 Short break Session on Statistics - Chair: J. Kececioglu -------------------------------------------- 15:05 Searching Gene Transfers on Bacillus Subtilis Using Hidden Markov Models L. Bize, F. Muri, F. Samson, F. Rodolphe, S. D. Ehrlich, B. Prum, P. Bessieres 15:30 Significance Testing for Genomic Mismatch Scanning G. R. Grant, R. S. Spielman, E. Manduchi, V. G. Cheung, W. J. Ewens 15h55 Break Session on Statistics - Chair: G. Kucherov ------------------------------------------ 16:20 Classifying Proteins by Family Using the Product of Correlated p-values T. L. Bailey, W. N. Grundy 16:45 Sequence Homology Detection Through Large Scale Pattern Discovery A. Floratos, I. Rigoutsos, L. Parida, G. Stolovitzky, Y. Gao 17:30 - 19:30 Poster Session ---------------------------- ----------------------- Tuesday, April 13, 1999 ----------------------- Plenary Lecture Session - Chair: D. Kahn ------------------------------------------- 8:30 Genome Sequences and Protein Structures Cyrus Chothia 9:30 Short break Session on Mapping - Chair: R. Karp ----------------------------------- 9:35 Algorithms for Whole Genome Shotgun Sequencing E. Anson, G. Myers 10:00 Construction of Physical Maps from Oligonucleotide Fingerprints Data G. Mayraz, R. Shamir 10:25 Computing Physical Maps of Chromosomes with Nonoverlapping Probes by Branch-and-Cut T. Christof, J. Kececioglu 10:50 Break Session on Threading - Chair: M. Vingron ---------------------------------------- 11:15 A Method for Optimal Design of a Threading Scoring Function J. R. Bienkowska, R. G. Rogers Jr., T. F. Smith 11:40 An Anytime Algorithm for Gapped Block Protein Threading with Pair Interactions R. H. Lathrop 12:05 Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes J. M. Kleinberg 12:30 - 14:00 Lunch ------------------- Lecture Session - Chair: S. Istrail ----------------------------------- 14:00 Trends in Computational Biology John Wooley 15:00 Short break Session on Sequence Alignment - Chair: A. Apostolico ---------------------------------------------------- 15:05 An Analytic Study of the Phase Transition Line in Local Sequence Alignment with Gaps R. Bundschuh, T. Hwa 15:30 Winnowing Sequences from a Database Search P. Berman, Z. Zhang, Y. I. Wolf, E. V. Koonin, W. Miller 15:55 q-gram Based Database Searching Using a Suffix Array (QUASAR) S. Burkhardt, A. Crauser, P. Ferragina, H-P. Lenhof, E. Rivals, M. Vingron 16:20 Break 16:45 Stanislaw Ulam - Computational Biology Address - Chair: M. Waterman Comparison of Complete Genomes: Organisation and Evolution Piotr Slonimski 18:00 - 23:00 Evening program at Saint-Romain-en-Gal ---------------------------------------------------- 18:00 Departure to Saint-Romain-en-Gal 19:00 Visit of the Museum 20:00 Cocktail offered by the Conseil General du Rhone ------------------------- Wednesday, April 14, 1999 ------------------------- Plenary Lecture Session: Chair R. Shamir ---------------------------------------- 9:00 Comparing Genes and Genomes: From Polymorphism to Phylogeny Peer Bork 10:00 Short break Session on Drug Design - Chair: R. Lathrop ------------------------------------------ 10:05 Efficient Database Screening for Rational Drug Design Using Pharmacophore-Constrained Conformational Search S. M. LaValle, L. E. Kavraki, P. W. Finn, J-C. Latombe 10:30 Coupled Optimization in Protein Docking J. C. Mitchell, A. T. Phillips, J. B. Rosen, L. F. Ten Eyck 10:55 Derivation of Sensitive Discrimination Potential for Virtual Ligand Screening M. Totrov, R. Abagyan 11:20 Break Session on Molecular Structure - Chair: J.M. Claverie ----------------------------------------------------- 11:45 Optimizing Combinatorial Library Construction via Split Synthesis B. Cohen, S. Skiena 12:10 Internal Loops in RNA Secondary Structure Prediction R. B. Lyngso, M. Zuker, C. N. S. Pedersen 12:35 - 14:00 Lunch Session on Gene Networks - Chair: T. Lengauer --------------------------------------------- 14:00 Identifying Gene Regulatory Networks from Experimental Data T. Chen, V. Filkov, S. S. Skiena 14:25 Evolution of Metabolisms: A New Method for the Comparison of Metabolic Pathways C. V. Forst, K. Schulten 14:50 Clustering Gene Expression Patterns A. Ben-Dor, Z. Yakhini 15:15 Closing session 15:30 End of the conference